Running as unit: rb-build-amd64_29-21133.service ==================================================================================== Fri Sep 27 02:22:37 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Fri Sep 27 02:22:37 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-2CQKERog" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 02:22:37 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 27 02:22:37 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-XBXPIv' Fri Sep 27 02:22:39 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 27 02:22:39 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-x1O9kY' ok, let's check if shasta is building anywhere yet… ok, shasta is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of shasta in trixie on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Fri Sep 27 02:22:57 UTC 2024 I: starting to build shasta/trixie/amd64 on jenkins on '2024-09-27 02:22' Fri Sep 27 02:22:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/21133/console.log 1727403777 amd64 trixie shasta Fri Sep 27 02:22:57 UTC 2024 I: Downloading source for trixie/shasta=0.12.0-1 --2024-09-27 02:22:57-- http://deb.debian.org/debian/pool/main/s/shasta/shasta_0.12.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2556 (2.5K) [text/prs.lines.tag] Saving to: ‘shasta_0.12.0-1.dsc’ 0K .. 100% 220M=0s 2024-09-27 02:22:57 (220 MB/s) - ‘shasta_0.12.0-1.dsc’ saved [2556/2556] --2024-09-27 02:22:57-- http://deb.debian.org/debian/pool/main/s/shasta/shasta_0.12.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2556 (2.5K) [text/prs.lines.tag] Saving to: ‘shasta_0.12.0-1.dsc’ 0K .. 100% 220M=0s 2024-09-27 02:22:57 (220 MB/s) - ‘shasta_0.12.0-1.dsc’ saved [2556/2556] Fri Sep 27 02:22:57 UTC 2024 I: shasta_0.12.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shasta Binary: shasta, python3-shasta, python3-shasta-doc Architecture: any-amd64 arm64 all Version: 0.12.0-1 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust , Étienne Mollier Homepage: https://github.com/chanzuckerberg/shasta Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/shasta Vcs-Git: https://salsa.debian.org/med-team/shasta.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev [any-amd64], libcereal-dev, libblas-dev, liblapack-dev, gfortran Package-List: python3-shasta deb python optional arch=any-amd64,arm64 python3-shasta-doc deb doc optional arch=all shasta deb science optional arch=any-amd64,arm64 Checksums-Sha1: 468ada59ae9bce71bf11ff0a2e109fa1ad9977e7 9602137 shasta_0.12.0.orig.tar.gz 211503e8daf13ec3a1e1f5e1a56d4e9f03355247 10120 shasta_0.12.0-1.debian.tar.xz Checksums-Sha256: 39a7fcc49df93d903d8a1ed21a57a7533fc44897cb58194bfd089356f36cfdc9 9602137 shasta_0.12.0.orig.tar.gz 2ed0b0cd1b6ac9960b92a3b26e7ab1be5e58c13fe65c4fdb20a75caeb2d07333 10120 shasta_0.12.0-1.debian.tar.xz Files: 6f61f2536ecadcb827b822af5d22f8a6 9602137 shasta_0.12.0.orig.tar.gz 52c1981c540bf79fc17ca6b60885c04c 10120 shasta_0.12.0-1.debian.tar.xz Dgit: 77c67b611fa7811c48fd7ca1fafff3a53b31a816 debian archive/debian/0.12.0-1 https://git.dgit.debian.org/shasta -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZTYYYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpdfg//XE2eew/aF0eEanRKG15kz1g+SheC /YAtH1XbXtQpH7FX1MDhWHP5K7n68DqsXG7Gyw0arZAthezEYn/xyZXxBh09sgwm x4k9F8e5u2lDWlqcIhqTh4j2VsdVG6/dGBEqnDdgvlQ9YIIGHdMlmrgQ3glHQjVS BhcaVMdTPXfV9lo1w3WFxYjU/sEC0OEvuGQX49Uu5oE0nu7tAHAno6es1zelaXHI 8AHRPlDVTCZhMPV4TDljAmjvpEbAWK/HsqVaamoqpwTPcJbpgI/XrGIVp2Ws/y+b BTWmJNHWvS1u8DojftcOjrywuVckMkVUqoYbEzUq5QUYhLJaso+Nzq4BE9BHzdne LCfJXuvISxcSkNX+3eMJWwOiUz6CMR/LyI2iXRvZkbkUWoJT0Hr+rp0CWnnzBgKF LAJEtAi+K+3koZAXM53rKrblcKsroXuKwSrOvuqqcv5CwJetvN2Wg1ZCAqP1vshb IobvMeSUX1O7++Qp6xYYbhKn6uwLjMpY4mm5xkjum/U4WQ52iOnCIQOLD3n+bNze 5+XKpaktXooPx2a685JTvl4pzQjajt8Y1bdyVuVSRbuLpbiE3886jb9Bx1Rcg6rC hQRFQOw352bmpI8fvCi81NEsR3Jm0yrGcVo/ZJz56rMeZMQLvUvG+eHHcXzh44MG 9l5k8BdLVrmpRfY= =ys3d -----END PGP SIGNATURE----- Fri Sep 27 02:22:57 UTC 2024 I: Checking whether the package is not for us Fri Sep 27 02:22:57 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Sep 27 02:22:57 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Sep 27 02:22:57 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 27 02:22:57 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-WuRyZN' ==================================================================================== Fri Sep 27 02:22:59 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 shasta trixie /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r 0.12.0-1" as arguments. Fri Sep 27 02:22:59 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-Dcg4cEhD" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 02:23:00 UTC 2024 I: Downloading source for trixie/shasta=0.12.0-1 Reading package lists... NOTICE: 'shasta' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/shasta.git Please use: git clone https://salsa.debian.org/med-team/shasta.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 9615 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (dsc) [2556 B] Get:2 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (tar) [9602 kB] Get:3 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (diff) [10.1 kB] Fetched 9615 kB in 0s (40.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'shasta' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/shasta.git Please use: git clone https://salsa.debian.org/med-team/shasta.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 9615 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (dsc) [2556 B] Get:2 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (tar) [9602 kB] Get:3 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (diff) [10.1 kB] Fetched 9615 kB in 0s (40.9 MB/s) Download complete and in download only mode ============================================================================= Building shasta in trixie on amd64 on ionos1-amd64 now. Date: Fri Sep 27 02:23:00 UTC 2024 Date UTC: Fri Sep 27 02:23:00 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 14:23:02 -12 2024 I: pbuilder-time-stamp: 1727403782 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shasta_0.12.0-1.dsc] I: copying [./shasta_0.12.0.orig.tar.gz] I: copying [./shasta_0.12.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun May 26 16:21:26 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shasta_0.12.0-1.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.12.0 dpkg-source: info: unpacking shasta_0.12.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5cf5c8dababf4f5ba362217857db9dc4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4149269' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_YJBn --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev, libcereal-dev, libblas-dev, liblapack-dev, gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on patchelf; however: Package patchelf is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on libcpu-features-dev; however: Package libcpu-features-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} cpp-13{a} cpp-13-x86-64-linux-gnu{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gcc-13{a} gcc-13-base{a} gcc-13-x86-64-linux-gnu{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcereal-dev{a} libcom-err2{a} libcpu-features-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgcc-13-dev{a} libgfortran-13-dev{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ncbi-blast+{a} ncbi-data{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchelf{a} po-debconf{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libpng-tools libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 316 newly installed, 0 to remove and 0 not upgraded. Need to get 266 MB of archives. After unpacking 1319 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1 [78.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.8p1-8 [965 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1 [349 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-1 [352 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.3-1 [2221 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.3-1 [11.4 MB] Get: 65 http://deb.debian.org/debian trixie/main amd64 gcc-13-base amd64 13.3.0-6 [47.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 cpp-13-x86-64-linux-gnu amd64 13.3.0-6 [9934 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 cpp-13 amd64 13.3.0-6 [1276 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgcc-13-dev amd64 13.3.0-6 [2538 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 gcc-13-x86-64-linux-gnu amd64 13.3.0-6 [19.2 MB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gcc-13 amd64 13.3.0-6 [496 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 77 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-3 [880 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-3 [11.7 MB] Get: 100 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-3 [11.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2 [1284 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:14.1.0-2 [1436 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.3.0-6 [847 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.3.0-6 [10.6 MB] Get: 105 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.3.0-6 [14.3 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-5 [207 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3.2 [240 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 130 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83.0 amd64 1.83.0-3.2 [259 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83-dev amd64 1.83.0-3.2 [264 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 133 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2 [333 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.2 [372 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3.2 [239 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83-dev amd64 1.83.0-3.2 [231 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2 [269 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83-dev amd64 1.83.0-3.2 [276 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83.0 amd64 1.83.0-3.2 [231 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83-dev amd64 1.83.0-3.2 [232 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 144 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 148 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 149 http://deb.debian.org/debian trixie/main amd64 libboost-exception1.83-dev amd64 1.83.0-3.2 [230 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 151 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2 [281 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3.2 [297 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83.0 amd64 1.83.0-3.2 [254 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83-dev amd64 1.83.0-3.2 [265 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83.0 amd64 1.83.0-3.2 [359 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83.0 amd64 1.83.0-3.2 [329 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-5 [10.4 MB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83-dev amd64 1.83.0-3.2 [346 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83.0 amd64 1.83.0-3.2 [471 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83-dev amd64 1.83.0-3.2 [541 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83-dev amd64 1.83.0-3.2 [382 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2 [70.2 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.0-2 [162 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.0-2 [17.9 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.3-2 [658 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83.0 amd64 1.83.0-3.2 [271 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-3.2 [280 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-3.2 [284 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3.2 [261 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83.0 amd64 1.83.0-3.2 [356 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83-dev amd64 1.83.0-3.2 [373 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 197 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83.0 amd64 1.83.0-3.2 [472 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83-dev amd64 1.83.0-3.2 [554 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 200 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83.0 amd64 1.83.0-3.2 [709 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83-dev amd64 1.83.0-3.2 [879 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 203 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83.0 amd64 1.83.0-3.2 [523 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83-dev amd64 1.83.0-3.2 [569 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 206 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.11.0-2 [251 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.3-2 [3954 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 225 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83-dev amd64 1.83.0-3.2 [290 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 227 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2 [306 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get: 229 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-3.2 [357 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-3.2 [237 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 235 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2 [242 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 238 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2 [347 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3.2 [375 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 241 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.5-1+b1 [10.1 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.5-1+b1 [26.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2 [327 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83.0 amd64 1.83.0-3.2 [238 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83-dev amd64 1.83.0-3.2 [240 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 254 http://deb.debian.org/debian trixie/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 255 http://deb.debian.org/debian trixie/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 256 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-3.2 [283 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 259 http://deb.debian.org/debian trixie/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 260 http://deb.debian.org/debian trixie/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 262 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2 [235 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 265 http://deb.debian.org/debian trixie/main amd64 libboost1.83-tools-dev amd64 1.83.0-3.2 [1529 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-3.2 [245 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-3.2 [249 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 270 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83.0 amd64 1.83.0-3.2 [336 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83-dev amd64 1.83.0-3.2 [422 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 273 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83.0 amd64 1.83.0-3.2 [437 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83-dev amd64 1.83.0-3.2 [486 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 277 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libcpu-features-dev amd64 0.9.0-1+b1 [22.0 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-1 [280 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.44-1 [362 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2 [70.5 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libspoa-dev amd64 4.1.4-2 [9532 B] Get: 292 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get: 294 http://deb.debian.org/debian trixie/main amd64 patchelf amd64 0.18.0-1.1 [97.1 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.5-1 [203 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30-1 [159 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.3.2-4 [117 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 307 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.5-1 [213 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-3 [588 kB] Fetched 266 MB in 21s (12.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2) ... Setting up libboost-serialization1.83.0:amd64 (1.83.0-3.2) ... Setting up libboost-numpy1.83.0 (1.83.0-3.2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up gcc-13-base:amd64 (13.3.0-6) ... Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libexpat1-dev:amd64 (2.6.3-1) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libboost-chrono1.83.0t64:amd64 (1.83.0-3.2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up libspoa7.0.0:amd64 (4.1.4-2) ... Setting up libboost-nowide1.83-dev (1.83.0-3.2) ... 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libboost-math1.83.0:amd64 (1.83.0-3.2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up patchelf (0.18.0-1.1) ... Setting up libfido2-1:amd64 (1.15.0-1) ... Setting up libgfortran-13-dev:amd64 (13.3.0-6) ... Setting up openssl (3.3.2-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:amd64 (72.1-5) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libboost1.83-tools-dev (1.83.0-3.2) ... Setting up chrpath (0.16-2+b1) ... 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Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-3.2) ... Setting up openssh-client (1:9.8p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-type-erasure1.83-dev:amd64 (1.83.0-3.2) ... Setting up libboost-random-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-locale-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-wave-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libhwloc-plugins:amd64 (2.11.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.1.0-2) ... Setting up libboost-graph1.83-dev:amd64 (1.83.0-3.2) ... Setting up gfortran (4:14.1.0-2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libboost-container-dev:amd64 (1.83.0.2+b2) ... 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Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up libboost-graph-dev:amd64 (1.83.0.2+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libboost-context-dev:amd64 (1.83.0.2+b2) ... Setting up libibverbs-dev:amd64 (52.0-2) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up gfortran-13 (13.3.0-6) ... Setting up libhsa-runtime64-1:amd64 (5.7.1-3) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up libamdhip64-5 (5.7.1-3) ... 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Setting up libboost-mpi1.83.0 (1.83.0-3.2) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-pybind11 (2.13.5-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up libboost-graph-parallel1.83.0 (1.83.0-3.2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up mpi-default-bin (1.17) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (5.5s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o [ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Assembler.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Assembler.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ 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CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 14%] Building CXX object 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&& /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp [ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMode3.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp [ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ 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-D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph1.cpp [ 44%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalReadGraph.cpp [ 44%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 45%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 45%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 45%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp [ 46%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 46%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LongBaseSequence.cpp [ 46%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LowHash0.cpp [ 46%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp [ 48%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MarkerFinder.cpp [ 48%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MarkerGraph.cpp [ 48%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp [ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.cpp [ 50%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/enumeratePaths.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 65%] 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/build/reproducible-path/shasta-0.12.0/src/extractKmer.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp [ 67%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/filesystem.cpp [ 67%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/globalMsa.cpp [ 67%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/html.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/longestPath.cpp [ 68%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mappedCopy.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/markerAccessFunctions.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-AssemblyGraph.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasedComponent.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o cd 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CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/platformDependent.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/runCommandWithTimeout.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/shastaLapack.cpp [ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSpoa.cpp [ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/timestamp.cpp [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp [ 99%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o 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CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 99%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/reproducible-path/shasta-0.12.0/srcMain/main.cpp [ 99%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.12 -ldl -lm [100%] Linking CXX static library shasta.a cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 /usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable /usr/bin/ranlib shasta.a make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaStaticLibrary make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v7.4.7 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: 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/build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/QuickStart.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ReportingBugs.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ComputationalMethods.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Configurations.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Mode3-0.12.0.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Acknowledgments.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ReadGraph1.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Commands.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Prerequisites.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BuildingFromSource.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-6.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CommandLineOptions.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignmentUnmarked.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/SupportedPlatforms.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PhasedRegionsNaming.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignment.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/4.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/3.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/6.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/7.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/2.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/1.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults-Images/5.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ChooseMemoryOptions.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/style.css -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MakeRelease.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Performance.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Python.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Running.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Compatibility.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/InspectingResults.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/conf.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/Makefile -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/shasta.so -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/index.rst -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PythonApi/README -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Mode3Chain.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-Before.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-5.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerAlignment.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/index.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Shasta-0.12.0.pdf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CZI-new-logo.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-After.png make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:418: renaming shasta.so to shasta.cpython-312-x86_64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' patchelf \ --set-soname shasta.cpython-312-x86_64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/reproducible-path/shasta-0.12.0 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-312-x86_64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4149269 and its subdirectories I: Current time: Thu Sep 26 14:46:25 -12 2024 I: pbuilder-time-stamp: 1727405185 Fri Sep 27 02:46:25 UTC 2024 I: Signing ./b1/shasta_0.12.0-1_amd64.buildinfo as shasta_0.12.0-1_amd64.buildinfo.asc Fri Sep 27 02:46:25 UTC 2024 I: Signed ./b1/shasta_0.12.0-1_amd64.buildinfo as ./b1/shasta_0.12.0-1_amd64.buildinfo.asc Fri Sep 27 02:46:25 UTC 2024 - build #1 for shasta/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Fri Sep 27 02:46:25 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Dcg4cEhD, removing. /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 02:46 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 02:22 b2 -rw------- 1 jenkins jenkins 3650 Sep 27 02:22 rbuildlog.V5uhqD2 -rw-r--r-- 1 jenkins jenkins 2556 May 26 16:33 shasta_0.12.0-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1: total 12876 -rw-r--r-- 1 jenkins jenkins 465650 Sep 27 02:46 build.log -rw-r--r-- 1 jenkins jenkins 134144 Sep 27 02:46 python3-shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 24072 Sep 27 02:46 python3-shasta-doc_0.12.0-1_all.deb -rw-r--r-- 1 jenkins jenkins 2250156 Sep 27 02:46 python3-shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 8280 Sep 27 02:46 shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 10120 Sep 27 02:46 shasta_0.12.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2556 Sep 27 02:46 shasta_0.12.0-1.dsc -rw-r--r-- 1 jenkins jenkins 16059 Sep 27 02:46 shasta_0.12.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 16941 Sep 27 02:46 shasta_0.12.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2539 Sep 27 02:46 shasta_0.12.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 625288 Sep 27 02:46 shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1601 Sep 27 02:46 shasta_0.12.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 9602137 Sep 27 02:46 shasta_0.12.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2: total 0 Fri Sep 27 02:46:30 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 14:23:02 -12 2024 I: pbuilder-time-stamp: 1727403782 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shasta_0.12.0-1.dsc] I: copying [./shasta_0.12.0.orig.tar.gz] I: copying [./shasta_0.12.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun May 26 16:21:26 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shasta_0.12.0-1.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.12.0 dpkg-source: info: unpacking shasta_0.12.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5cf5c8dababf4f5ba362217857db9dc4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4149269' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_YJBn --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev, libcereal-dev, libblas-dev, liblapack-dev, gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on patchelf; however: Package patchelf is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on libcpu-features-dev; however: Package libcpu-features-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} cpp-13{a} cpp-13-x86-64-linux-gnu{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gcc-13{a} gcc-13-base{a} gcc-13-x86-64-linux-gnu{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcereal-dev{a} libcom-err2{a} libcpu-features-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgcc-13-dev{a} libgfortran-13-dev{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ncbi-blast+{a} ncbi-data{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchelf{a} po-debconf{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libpng-tools libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 316 newly installed, 0 to remove and 0 not upgraded. Need to get 266 MB of archives. After unpacking 1319 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1 [78.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.8p1-8 [965 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1 [349 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-1 [352 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.3-1 [2221 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.3-1 [11.4 MB] Get: 65 http://deb.debian.org/debian trixie/main amd64 gcc-13-base amd64 13.3.0-6 [47.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 cpp-13-x86-64-linux-gnu amd64 13.3.0-6 [9934 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 cpp-13 amd64 13.3.0-6 [1276 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgcc-13-dev amd64 13.3.0-6 [2538 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 gcc-13-x86-64-linux-gnu amd64 13.3.0-6 [19.2 MB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gcc-13 amd64 13.3.0-6 [496 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 77 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-3 [880 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-3 [11.7 MB] Get: 100 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-3 [11.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2 [1284 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:14.1.0-2 [1436 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.3.0-6 [847 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.3.0-6 [10.6 MB] Get: 105 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.3.0-6 [14.3 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-5 [207 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3.2 [240 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 130 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83.0 amd64 1.83.0-3.2 [259 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83-dev amd64 1.83.0-3.2 [264 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 133 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2 [333 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.2 [372 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3.2 [239 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83-dev amd64 1.83.0-3.2 [231 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2 [269 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83-dev amd64 1.83.0-3.2 [276 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83.0 amd64 1.83.0-3.2 [231 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83-dev amd64 1.83.0-3.2 [232 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 144 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 148 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 149 http://deb.debian.org/debian trixie/main amd64 libboost-exception1.83-dev amd64 1.83.0-3.2 [230 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 151 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2 [281 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3.2 [297 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83.0 amd64 1.83.0-3.2 [254 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83-dev amd64 1.83.0-3.2 [265 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83.0 amd64 1.83.0-3.2 [359 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83.0 amd64 1.83.0-3.2 [329 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-5 [10.4 MB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83-dev amd64 1.83.0-3.2 [346 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83.0 amd64 1.83.0-3.2 [471 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83-dev amd64 1.83.0-3.2 [541 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83-dev amd64 1.83.0-3.2 [382 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2 [70.2 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.0-2 [162 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.0-2 [17.9 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.3-2 [658 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83.0 amd64 1.83.0-3.2 [271 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-3.2 [280 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-3.2 [284 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3.2 [261 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83.0 amd64 1.83.0-3.2 [356 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83-dev amd64 1.83.0-3.2 [373 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 197 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83.0 amd64 1.83.0-3.2 [472 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83-dev amd64 1.83.0-3.2 [554 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 200 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83.0 amd64 1.83.0-3.2 [709 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83-dev amd64 1.83.0-3.2 [879 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 203 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83.0 amd64 1.83.0-3.2 [523 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83-dev amd64 1.83.0-3.2 [569 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 206 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.11.0-2 [251 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.3-2 [3954 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 225 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83-dev amd64 1.83.0-3.2 [290 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 227 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2 [306 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get: 229 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-3.2 [357 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-3.2 [237 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 235 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2 [242 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 238 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2 [347 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3.2 [375 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 241 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.5-1+b1 [10.1 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.5-1+b1 [26.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2 [327 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83.0 amd64 1.83.0-3.2 [238 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83-dev amd64 1.83.0-3.2 [240 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 254 http://deb.debian.org/debian trixie/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 255 http://deb.debian.org/debian trixie/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 256 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-3.2 [283 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 259 http://deb.debian.org/debian trixie/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 260 http://deb.debian.org/debian trixie/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 262 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2 [235 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 265 http://deb.debian.org/debian trixie/main amd64 libboost1.83-tools-dev amd64 1.83.0-3.2 [1529 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-3.2 [245 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-3.2 [249 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 270 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83.0 amd64 1.83.0-3.2 [336 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83-dev amd64 1.83.0-3.2 [422 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 273 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83.0 amd64 1.83.0-3.2 [437 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83-dev amd64 1.83.0-3.2 [486 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 277 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libcpu-features-dev amd64 0.9.0-1+b1 [22.0 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-1 [280 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.44-1 [362 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2 [70.5 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libspoa-dev amd64 4.1.4-2 [9532 B] Get: 292 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get: 294 http://deb.debian.org/debian trixie/main amd64 patchelf amd64 0.18.0-1.1 [97.1 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.5-1 [203 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30-1 [159 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.3.2-4 [117 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 307 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.5-1 [213 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-3 [588 kB] Fetched 266 MB in 21s (12.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20103 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_amd64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21177 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1+b1_amd64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package sgml-base. 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libboost-math1.83.0:amd64 (1.83.0-3.2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up patchelf (0.18.0-1.1) ... Setting up libfido2-1:amd64 (1.15.0-1) ... Setting up libgfortran-13-dev:amd64 (13.3.0-6) ... Setting up openssl (3.3.2-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:amd64 (72.1-5) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libboost1.83-tools-dev (1.83.0-3.2) ... Setting up chrpath (0.16-2+b1) ... 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Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-3.2) ... Setting up libboost-exception-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-nowide-dev (1.83.0.2+b2) ... Setting up gfortran-13-x86-64-linux-gnu (13.3.0-6) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libboost-test-dev:amd64 (1.83.0.2+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-7+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:amd64 (1.83.0-3.2) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libboost-container1.83-dev:amd64 (1.83.0-3.2) ... 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (5.5s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu 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-D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o [ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign3.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAnalyzePaths.cpp [ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign5.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentCandidates.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignmentGraph.cpp [ 14%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlignments.cpp [ 16%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 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&& /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result 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-D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp [ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp [ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMode3.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG 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/usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/InducedAlignment.cpp [ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o cd 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp [ 39%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentCandidateGraph.cpp [ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAlignmentGraph.cpp [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion 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-Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.cpp [ 42%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerOptions.cpp [ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0.cpp [ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph1.cpp [ 44%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalReadGraph.cpp [ 44%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 45%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp [ 45%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ 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-I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/longestPath.cpp [ 68%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mappedCopy.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/markerAccessFunctions.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-AssemblyGraph.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-LocalAssembly.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasedComponent.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PrimaryGraph.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/performanceLog.cpp [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/platformDependent.cpp [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/runCommandWithTimeout.cpp [ 73%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/shastaLapack.cpp [ 73%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSpoa.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp [ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PeakFinder.cpp [ 82%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT 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Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp [ 99%] Linking CXX shared library shasta.so cd 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 99%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/reproducible-path/shasta-0.12.0/srcMain/main.cpp [ 99%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.12 -ldl -lm [100%] Linking CXX static library shasta.a cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 /usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable /usr/bin/ranlib shasta.a make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaStaticLibrary make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v7.4.7 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: 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/build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-5.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerAlignment.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/index.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Shasta-0.12.0.pdf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CZI-new-logo.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-After.png make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:418: renaming shasta.so to shasta.cpython-312-x86_64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' patchelf \ --set-soname shasta.cpython-312-x86_64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/reproducible-path/shasta-0.12.0 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-312-x86_64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4149269 and its subdirectories I: Current time: Thu Sep 26 14:46:25 -12 2024 I: pbuilder-time-stamp: 1727405185 Fri Sep 27 02:46:30 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Sep 27 02:46:30 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Sep 27 02:46:30 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 27 02:46:30 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-le2zIf' ==================================================================================== Thu Oct 30 09:09:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 shasta trixie /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r 0.12.0-1" as arguments. Thu Oct 30 09:09:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-wDMolb59" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Oct 30 09:09:32 UTC 2025 I: Downloading source for trixie/shasta=0.12.0-1 Reading package lists... NOTICE: 'shasta' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/shasta.git Please use: git clone https://salsa.debian.org/med-team/shasta.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 9615 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (dsc) [2556 B] Get:2 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (tar) [9602 kB] Get:3 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (diff) [10.1 kB] Fetched 9615 kB in 0s (56.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'shasta' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/shasta.git Please use: git clone https://salsa.debian.org/med-team/shasta.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 9615 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (dsc) [2556 B] Get:2 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (tar) [9602 kB] Get:3 http://deb.debian.org/debian trixie/main shasta 0.12.0-1 (diff) [10.1 kB] Fetched 9615 kB in 0s (56.6 MB/s) Download complete and in download only mode ============================================================================= Re-Building shasta in trixie on amd64 on ionos15-amd64 now. Date: Thu Oct 30 09:09:32 UTC 2025 Date UTC: Thu Oct 30 09:09:32 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_R30Z + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' shasta = debian-installer -o shasta = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' shasta = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_R30Z --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2 --logfile b2/build.log shasta_0.12.0-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 30 23:09:32 +14 2025 I: pbuilder-time-stamp: 1761815372 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shasta_0.12.0-1.dsc] I: copying [./shasta_0.12.0.orig.tar.gz] I: copying [./shasta_0.12.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun May 26 16:21:26 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shasta_0.12.0-1.dsc: no acceptable signature found dpkg-source: info: extracting shasta in shasta-0.12.0 dpkg-source: info: unpacking shasta_0.12.0.orig.tar.gz dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 30 09:09 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6e78863ea56d4a00a649129d3b9debc8 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2943006 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_R30Z --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2 --logfile b2/build.log shasta_0.12.0-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev:native, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcpu-features-dev, libcereal-dev, libblas-dev, liblapack-dev, gfortran dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on patchelf; however: Package patchelf is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on libcpu-features-dev; however: Package libcpu-features-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} cpp-13{a} cpp-13-x86-64-linux-gnu{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gcc-13{a} gcc-13-base{a} gcc-13-x86-64-linux-gnu{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcereal-dev{a} libcom-err2{a} libcpu-features-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgcc-13-dev{a} libgfortran-13-dev{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17t64{a} liblmdb0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ncbi-blast+{a} ncbi-data{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchelf{a} po-debconf{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libpng-tools libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget xauth 0 packages upgraded, 316 newly installed, 0 to remove and 0 not upgraded. Need to get 266 MB of archives. After unpacking 1319 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1 [78.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.8p1-8 [965 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1 [349 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-1 [352 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.3-1 [2221 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.3-1 [11.4 MB] Get: 65 http://deb.debian.org/debian trixie/main amd64 gcc-13-base amd64 13.3.0-6 [47.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 cpp-13-x86-64-linux-gnu amd64 13.3.0-6 [9934 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 cpp-13 amd64 13.3.0-6 [1276 B] Get: 68 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgcc-13-dev amd64 13.3.0-6 [2538 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 gcc-13-x86-64-linux-gnu amd64 13.3.0-6 [19.2 MB] Get: 71 http://deb.debian.org/debian trixie/main amd64 gcc-13 amd64 13.3.0-6 [496 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 77 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-3 [880 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-3 [11.7 MB] Get: 100 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-3 [11.8 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2 [1284 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:14.1.0-2 [1436 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.3.0-6 [847 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.3.0-6 [10.6 MB] Get: 105 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.3.0-6 [14.3 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-5 [207 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 115 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 127 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3.2 [240 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 130 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83.0 amd64 1.83.0-3.2 [259 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libboost-container1.83-dev amd64 1.83.0-3.2 [264 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 133 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2 [333 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3.2 [372 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3.2 [239 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83.0 amd64 1.83.0-3.2 [230 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83-dev amd64 1.83.0-3.2 [231 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2 [269 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83-dev amd64 1.83.0-3.2 [276 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83.0 amd64 1.83.0-3.2 [231 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libboost-context1.83-dev amd64 1.83.0-3.2 [232 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 144 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 148 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 149 http://deb.debian.org/debian trixie/main amd64 libboost-exception1.83-dev amd64 1.83.0-3.2 [230 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 151 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2 [281 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3.2 [297 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83.0 amd64 1.83.0-3.2 [254 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libboost-fiber1.83-dev amd64 1.83.0-3.2 [265 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 156 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 157 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83.0 amd64 1.83.0-3.2 [359 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83.0 amd64 1.83.0-3.2 [329 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-5 [10.4 MB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83-dev amd64 1.83.0-3.2 [346 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83.0 amd64 1.83.0-3.2 [471 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libboost-test1.83-dev amd64 1.83.0-3.2 [541 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libboost-graph1.83-dev amd64 1.83.0-3.2 [382 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2 [70.2 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.0-2 [162 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.0-2 [17.9 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.3-2 [658 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83.0 amd64 1.83.0-3.2 [271 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-3.2 [280 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-3.2 [284 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 192 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3.2 [261 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83.0 amd64 1.83.0-3.2 [356 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libboost-json1.83-dev amd64 1.83.0-3.2 [373 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 197 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83.0 amd64 1.83.0-3.2 [472 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libboost-locale1.83-dev amd64 1.83.0-3.2 [554 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 200 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83.0 amd64 1.83.0-3.2 [709 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libboost-log1.83-dev amd64 1.83.0-3.2 [879 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 203 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83.0 amd64 1.83.0-3.2 [523 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libboost-math1.83-dev amd64 1.83.0-3.2 [569 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 206 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.11.0-2 [251 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.3-2 [3954 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 225 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83-dev amd64 1.83.0-3.2 [290 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 227 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2 [306 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get: 229 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-3.2 [357 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-3.2 [237 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 232 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83.0 amd64 1.83.0-3.2 [234 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libboost-nowide1.83-dev amd64 1.83.0-3.2 [235 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 235 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2 [242 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 238 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2 [347 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3.2 [375 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 241 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.5-1+b1 [10.1 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.5-1+b1 [26.1 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2 [327 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 251 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83.0 amd64 1.83.0-3.2 [238 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libboost-random1.83-dev amd64 1.83.0-3.2 [240 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 254 http://deb.debian.org/debian trixie/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 255 http://deb.debian.org/debian trixie/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 256 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-3.2 [283 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-3.2 [245 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 259 http://deb.debian.org/debian trixie/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 260 http://deb.debian.org/debian trixie/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 261 http://deb.debian.org/debian trixie/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 262 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2 [235 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83-dev amd64 1.83.0-3.2 [236 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 265 http://deb.debian.org/debian trixie/main amd64 libboost1.83-tools-dev amd64 1.83.0-3.2 [1529 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 267 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-3.2 [245 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-3.2 [249 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 270 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83.0 amd64 1.83.0-3.2 [336 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libboost-url1.83-dev amd64 1.83.0-3.2 [422 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 273 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83.0 amd64 1.83.0-3.2 [437 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libboost-wave1.83-dev amd64 1.83.0-3.2 [486 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 276 http://deb.debian.org/debian trixie/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 277 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libcpu-features-dev amd64 0.9.0-1+b1 [22.0 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-1 [280 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.44-1 [362 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2 [70.5 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libspoa-dev amd64 4.1.4-2 [9532 B] Get: 292 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get: 294 http://deb.debian.org/debian trixie/main amd64 patchelf amd64 0.18.0-1.1 [97.1 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.5-1 [203 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30-1 [159 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.3.2-4 [117 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 307 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.5-1 [213 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 313 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 314 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-3 [588 kB] Fetched 266 MB in 3s (96.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20103 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_amd64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21177 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1+b1_amd64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-1_amd64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... 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Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../027-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../028-libarchive13t64_3.7.4-1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../029-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../030-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../031-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../032-libldap-2.5-0_2.5.18+dfsg-3_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../033-libnghttp2-14_1.63.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.63.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../034-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../035-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../036-libssh2-1t64_1.11.0-7_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-7) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../037-libcurl4t64_8.10.1-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.10.1-1) ... 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Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-3.2) ... Setting up openssh-client (1:9.8p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-type-erasure1.83-dev:amd64 (1.83.0-3.2) ... Setting up libboost-random-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-locale-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-wave-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libhwloc-plugins:amd64 (2.11.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.1.0-2) ... Setting up libboost-graph1.83-dev:amd64 (1.83.0-3.2) ... Setting up gfortran (4:14.1.0-2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libboost-container-dev:amd64 (1.83.0.2+b2) ... 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Setting up libboost-mpi1.83.0 (1.83.0-3.2) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-pybind11 (2.13.5-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up libboost-graph-parallel1.83.0 (1.83.0-3.2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up mpi-default-bin (1.17) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-3.2) ... Setting up dh-python (6.20240824) ... Setting up libboost-mpi-python1.83.0 (1.83.0-3.2) ... Setting up libboost-graph-parallel-dev (1.83.0.2+b2) ... Setting up mpi-default-dev (1.17) ... Setting up libboost-mpi1.83-dev (1.83.0-3.2) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-3.2) ... Setting up libboost-mpi-python-dev (1.83.0.2+b2) ... Setting up libboost-all-dev (1.83.0.2+b2) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../shasta_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary dh binary --with python3,sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_configure -- -DBUILD_ID=0.12.0 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_ID=0.12.0 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is x86_64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 -- Configuring done (0.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o [ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o [ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o [ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o [ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp [ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG 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-DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/PngImage.hpp:6, from /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::distance’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::distance’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = pair; _Args = {pair}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘constexpr std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/vector.tcc:117:30, inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_vector.h:1301:21, inlined from ‘shasta::CompactUndirectedGraph::vertex_descriptor shasta::CompactUndirectedGraph::addVertex(const Vertex&) [with Vertex = shasta::AlignmentGraphVertex; Edge = shasta::AlignmentGraphEdge]’ at /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.hpp:500:26, inlined from ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’ at /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:239:34: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘vertex.shasta::AlignmentGraphVertex::color’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp: In member function ‘void shasta::AlignmentGraph::createVertices(const std::array, 2>&, uint32_t)’: /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp [ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp [ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Alignments.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp [ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API 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-DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c 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-MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 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-D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong 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-I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp [ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkers.cpp [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API 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-DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 30%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp [ 37%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp [ 38%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompactUndirectedGraph.cpp [ 39%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp [ 39%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/shasta-0.12.0/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:11, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1694:53: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/LocalAssemblyGraph.hpp:18, from /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:6: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = boost::list_edge; _Args = {const boost::list_edge&}]’, inlined from ‘static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge; _Args = {const boost::list_edge&}; _Tp = std::_List_node >]’ at /usr/include/c++/14/bits/alloc_traits.h:536:21, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:713:33, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge&}; _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:2004:32, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge; _Alloc = std::allocator >]’ at /usr/include/c++/14/bits/stl_list.h:1306:24, inlined from ‘std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:574:20, inlined from ‘std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list, std::allocator > >; T = boost::list_edge&]’ at /usr/include/boost/pending/container_traits.hpp:606:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1498:29, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::LocalAssemblyGraphVertex, shasta::LocalAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’ at /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph.cpp:1739:57: /usr/include/c++/14/bits/stl_construct.h:97:14: warning: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘bool shasta::Assembler::extractLocalAssemblyGraph(shasta::mode0::AssemblyGraph::EdgeId, int, double, shasta::LocalAssemblyGraph&) const’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ [ 40%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp [ 41%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ConfigurationTable.cpp [ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Reads.cpp [ 65%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MedianConsensusCaller.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReferenceOverlapMap.cpp [ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ShortBaseSequence.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SimpleBayesianConsensusCaller-Builtin.cpp [ 67%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SimpleBayesianConsensusCaller.cpp [ 67%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SimpleConsensusCaller.cpp [ 68%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/assembleMarkerGraphPath.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MemoryMappedAllocator.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MemoryMappedVector.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Mode3Assembler.cpp [ 69%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/buildId.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255, from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:14: /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1496:48, inlined from ‘std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::CompressedAssemblyGraphVertex, shasta::CompressedAssemblyGraphEdge, no_property, listS>::config]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1522:20, inlined from ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’ at /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:200:43: /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.hpp:47:15: warning: ‘p.shasta::CompressedAssemblyGraphEdge::maxMarkerCount’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class shasta::CompressedAssemblyGraphEdge { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/graph/detail/adjacency_list.hpp: In member function ‘void shasta::CompressedAssemblyGraph::mergeLinearChains()’: /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MultithreadedObject.cpp [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/runCommandWithTimeout.cpp [ 97%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API 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CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o /usr/bin/ranlib shasta.a make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaStaticLibrary [100%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/reproducible-path/shasta-0.12.0/srcMain/main.cpp [100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v7.4.7 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.a -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/shasta.so -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/shastaDynamic -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads1.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AlignOrientedReads4.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeAlignmentMatrix.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeAssemblyGraphBubbles.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AnalyzeReadGraph.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/Assemble.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/AssembleMarkerGraphEdges.py -- Installing: 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/build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Performance.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BuildingFromSource.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PhasedRegionsNaming.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Acknowledgments.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignmentUnmarked.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Configurations.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Markers.png make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_install -Nshasta -Npython3-shasta dh_installdocs dh_sphinxdoc dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 fs:418: renaming shasta.so to shasta.cpython-312-x86_64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' patchelf \ --set-soname shasta.cpython-312-x86_64-linux-gnu.so \ /build/reproducible-path/shasta-0.12.0/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//build/reproducible-path/shasta-0.12.0 dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-x86_64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so # modify the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-312-x86_64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2943006 and its subdirectories I: Current time: Thu Oct 30 23:12:35 +14 2025 I: pbuilder-time-stamp: 1761815555 + false + set +x Thu Oct 30 09:12:35 UTC 2025 I: Signing ./b2/shasta_0.12.0-1_amd64.buildinfo as shasta_0.12.0-1_amd64.buildinfo.asc Thu Oct 30 09:12:36 UTC 2025 I: Signed ./b2/shasta_0.12.0-1_amd64.buildinfo as ./b2/shasta_0.12.0-1_amd64.buildinfo.asc Thu Oct 30 09:12:36 UTC 2025 - build #2 for shasta/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Oct 30 09:12:36 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-wDMolb59, removing. /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r: total 476 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 02:46 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 02:49 b2 -rw------- 1 jenkins jenkins 469588 Sep 27 02:46 rbuildlog.V5uhqD2 -rw-r--r-- 1 jenkins jenkins 2556 May 26 16:33 shasta_0.12.0-1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1: total 12908 -rw-r--r-- 1 jenkins jenkins 465650 Sep 27 02:46 build.log -rw-r--r-- 1 jenkins jenkins 134144 Sep 27 02:46 python3-shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 24072 Sep 27 02:46 python3-shasta-doc_0.12.0-1_all.deb -rw-r--r-- 1 jenkins jenkins 2250156 Sep 27 02:46 python3-shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 8280 Sep 27 02:46 shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 10120 Sep 27 02:46 shasta_0.12.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2556 Sep 27 02:46 shasta_0.12.0-1.dsc -rw-r--r-- 1 jenkins jenkins 16059 Sep 27 02:46 shasta_0.12.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 16941 Sep 27 02:46 shasta_0.12.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2539 Sep 27 02:46 shasta_0.12.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 625288 Sep 27 02:46 shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1601 Sep 27 02:46 shasta_0.12.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 9602137 Sep 27 02:46 shasta_0.12.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2: total 12880 -rw-r--r-- 1 jenkins jenkins 467591 Sep 27 02:49 build.log -rw-r--r-- 1 jenkins jenkins 134144 Sep 27 02:49 python3-shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 24072 Sep 27 02:49 python3-shasta-doc_0.12.0-1_all.deb -rw-r--r-- 1 jenkins jenkins 2250156 Sep 27 02:49 python3-shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 8280 Sep 27 02:49 shasta-dbgsym_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 10120 Sep 27 02:49 shasta_0.12.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2556 Sep 27 02:49 shasta_0.12.0-1.dsc -rw-r--r-- 1 jenkins jenkins 16068 Sep 27 02:49 shasta_0.12.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 16950 Sep 27 02:49 shasta_0.12.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2539 Sep 27 02:49 shasta_0.12.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 625288 Sep 27 02:49 shasta_0.12.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1601 Sep 27 02:49 shasta_0.12.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 9602137 Sep 27 02:49 shasta_0.12.0.orig.tar.gz Fri Sep 27 02:49:36 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Sep 27 02:49:37 UTC 2024 I: shasta_0.12.0-1_amd64.changes: Format: 1.8 Date: Sun, 26 May 2024 18:05:55 +0200 Source: shasta Binary: python3-shasta python3-shasta-dbgsym python3-shasta-doc shasta shasta-dbgsym Architecture: amd64 all Version: 0.12.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: python3-shasta - nanopore whole genome assembly (dynamic library) python3-shasta-doc - nanopore whole genome assembly (documentation) shasta - nanopore whole genome assembly (binaries and scripts) Changes: shasta (0.12.0-1) unstable; urgency=medium . * New upstream version 0.12.0 * gcc-13.patch: delete: applied upstream. * gcc-13-bis.patch: delete: applied upstream. * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: a01becf7df036dd0cb4135dcc5faaa077114c374 134144 python3-shasta-dbgsym_0.12.0-1_amd64.deb e7b7d3d0075c87a4b910a0f3ec3e0c3840b6e1d5 24072 python3-shasta-doc_0.12.0-1_all.deb c92f4c2c777907b9c4e0908b7c9eddf7a23817ed 2250156 python3-shasta_0.12.0-1_amd64.deb 8b7b8321da365e035fc746e223263cea7779b427 8280 shasta-dbgsym_0.12.0-1_amd64.deb ed19c28e4aac6b13903909ae08b188b4e4180fdc 16059 shasta_0.12.0-1_amd64.buildinfo c729bbdb377f96e19a448b3d83478e165e34b0e4 625288 shasta_0.12.0-1_amd64.deb Checksums-Sha256: 2e9b2d9724aeeb80c9123f4bf0fa1ce9c2e6174591234ae141948c9e52b0aebc 134144 python3-shasta-dbgsym_0.12.0-1_amd64.deb fb67a3e753693ef8f70f40be8d989be2abfed729caac98991241a9370b5ff26f 24072 python3-shasta-doc_0.12.0-1_all.deb d20de8dcef65d4ecf1f858a88d534be850fc1424f8c805e56e184e69972f80dd 2250156 python3-shasta_0.12.0-1_amd64.deb 727a82123b36c753690ee5101f84e4b7fa26691bd87b815e3d3995b8698376dd 8280 shasta-dbgsym_0.12.0-1_amd64.deb 86e4b5d6b14ff5186ba2a21af7ef8e2e3d1b9b1d4d8975ba22733b072d2c4ced 16059 shasta_0.12.0-1_amd64.buildinfo 3198318454c8096fba10b9e759f2eaeeea4e02e344c5fd3c48a5cdc4f33b2d5e 625288 shasta_0.12.0-1_amd64.deb Files: e43c9d7d3922bdea83a7e1e16f3c2797 134144 debug optional python3-shasta-dbgsym_0.12.0-1_amd64.deb b284ed0671625b30ebdc96d5e92c3c45 24072 doc optional python3-shasta-doc_0.12.0-1_all.deb de6235772f4e32fcb1c5f0ab6a75b8c7 2250156 python optional python3-shasta_0.12.0-1_amd64.deb 59908993e3bdfa21d555b9409858c2fd 8280 debug optional shasta-dbgsym_0.12.0-1_amd64.deb 9ca8e347a5a3c202b9e30b3bc3722bf3 16059 science optional shasta_0.12.0-1_amd64.buildinfo c05c270ccffaa1f7afe527251ae110db 625288 science optional shasta_0.12.0-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/shasta_0.12.0-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/shasta_0.12.0-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/shasta_0.12.0-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/shasta_0.12.0-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/shasta_0.12.0-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/shasta_0.12.0-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-27 02:46:29.960495565 +0000 +++ b2/build.log 2024-09-27 02:49:36.652556843 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 26 14:23:02 -12 2024 -I: pbuilder-time-stamp: 1727403782 +I: Current time: Thu Oct 30 23:09:32 +14 2025 +I: pbuilder-time-stamp: 1761815372 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 30 09:09 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5cf5c8dababf4f5ba362217857db9dc4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4149269' - PS1='# ' - PS2='> ' + INVOCATION_ID=6e78863ea56d4a00a649129d3b9debc8 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2943006 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_YJBn --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/pbuilderrc_R30Z --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2 --logfile b2/build.log shasta_0.12.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4149269/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -460,7 +492,7 @@ Get: 314 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 315 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-3 [731 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-3 [588 kB] -Fetched 266 MB in 21s (12.8 MB/s) +Fetched 266 MB in 3s (96.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) @@ -1479,8 +1511,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Sep 27 02:30:50 UTC 2024. -Universal Time is now: Fri Sep 27 02:30:50 UTC 2024. +Local time is now: Thu Oct 30 09:10:43 UTC 2025. +Universal Time is now: Thu Oct 30 09:10:43 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2) ... @@ -1773,7 +1805,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.12.0-1_source.changes +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../shasta_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable @@ -1814,8 +1850,8 @@ -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 --- Configuring done (5.5s) --- Generating done (0.2s) +-- Configuring done (0.5s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1834,7 +1870,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1852,50 +1888,94 @@ make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp [ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp -[ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +[ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o [ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp +[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o +[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o +[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o +[ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o +[ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o +[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp -[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp +[ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o +[ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp +[ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o +[ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp +[ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o +[ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o +[ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o +[ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o +[ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o +[ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o +[ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp -[ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp -[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 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-I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, @@ -1958,78 +2038,104 @@ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ +[ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-AssemblyGraph.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ -[ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ -[ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp +[ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, @@ -2077,28 +2183,6 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp -[ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp -[ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/ios:42, from /usr/include/c++/14/ostream:40, @@ -2146,74 +2230,126 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ -[ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MarkerGraph.cpp +[ 55%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReadLoader.cpp +[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o 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object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ReferenceOverlapMap.cpp +[ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.cpp +[ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/ShortBaseSequence.cpp In file included from 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-D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp +[ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/timestamp.cpp +[ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp +[100%] Linking CXX static library shasta.a +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 +/usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o +/usr/bin/ranlib shasta.a +make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' +[100%] Built target shastaStaticLibrary +[100%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[ 99%] Built target shastaDynamicLibrary +[100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o +[100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/reproducible-path/shasta-0.12.0/srcMain/main.cpp -[ 99%] Linking CXX executable shastaDynamic +[100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' [100%] Built target shastaDynamicExecutable -/usr/bin/ranlib shasta.a -make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[100%] Built target shastaStaticLibrary make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' @@ -2583,7 +2619,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2707,118 +2743,118 @@ -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/generateBandageLabelsFromAlignment.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/testGlobalMsa.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CLR-Dec2019.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/RemoveConflicts.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-3.csv +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Phased-Nov2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-5.csv +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-R10-Fast-Nov2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-8.csv -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CCS-Dec2019.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-10.csv --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-Aug2021.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Oct2021.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Jun2020.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/HiFi-Oct2021.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CLR-Dec2019.conf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-May2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Sep2020.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Jun2020.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-May2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/README.md +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-R10-Slow-Nov2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-2.csv -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Dec2019.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-10.csv +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-May2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-6.csv +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-OldGuppy-Sep2020.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Human-SingleFlowcell-May2022.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Dec2019.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Oct2021.conf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Sep2020.conf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Phased-Oct2021.conf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-iterative-Sep2020.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-11.csv --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Dec2019.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-UL-Jan2022.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/README.md --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/Nanopore-Phased-R10-Slow-Nov2022.conf --- Installing: 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/build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CommandLineOptions.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CZI-new-logo.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-After.png -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-5.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Introduction.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Prerequisites.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Shasta-0.12.0.pdf -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerAlignment.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/index.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-Before.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/QuickStart.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ComputationalMethods.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/ReadGraph2.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Bubble.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-6.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Running.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Commands.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChain.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Shasta-0.12.0.pdf +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Performance.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BuildingFromSource.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/PhasedRegionsNaming.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/BubbleChainPath.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Acknowledgments.html -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/CZI-new-logo.png --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Detangle-After.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/RawAlignmentUnmarked.png +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Configurations.html +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot +-- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Markers.png make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' @@ -2890,10 +2926,10 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. +dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. -dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2901,12 +2937,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2943006/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/4149269 and its subdirectories -I: Current time: Thu Sep 26 14:46:25 -12 2024 -I: pbuilder-time-stamp: 1727405185 +I: removing directory /srv/workspace/pbuilder/2943006 and its subdirectories +I: Current time: Thu Oct 30 23:12:35 +14 2025 +I: pbuilder-time-stamp: 1761815555 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/shasta_0.12.0-1.diff: 95.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/shasta_0.12.0-1.diff.gz b2/build.log: 92.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 92.0% -- replaced with stdout Fri Sep 27 02:49:38 UTC 2024 I: diffoscope 277 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_shasta_trixie_amd64_1727405378 + touch /var/log/reproducible-builds/diffoscope_stamp_shasta_trixie_amd64_1727405378 + RESULT=0 + systemd-run '--description=diffoscope on shasta/0.12.0-1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_29-21133 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r --run-session -c jenkins-reproducible-trixie-diffoscope-75da0f44-9a50-4576-8e92-9e84255b3455 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/dbd-tmp-fZqzMeL ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1/shasta_0.12.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2/shasta_0.12.0-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_29-21133.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/shasta_0.12.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b1/shasta_0.12.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.19WqkP1r/b2/shasta_0.12.0-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.423s) 0.423s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.051s) 0.051s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 757ms CPU time consumed: 757ms _ _ ___| |__ __ _ ___| |_ __ _ / __| '_ \ / _` / __| __/ _` | \__ \ | | | (_| \__ \ || (_| | |___/_| |_|\__,_|___/\__\__,_| Fri Sep 27 02:49:39 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 27 02:49:39 UTC 2024 I: shasta from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-27 02:49:40] INFO: Starting at 2024-09-27 02:49:40.461442 [2024-09-27 02:49:40] INFO: Generating the pages of 1 package(s) [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:40] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/shasta didn't produce a buildlog, even though it has been built. [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/shasta_0.11.1-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/shasta_0.11.1-1.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/shasta_0.11.1-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/shasta_0.11.1-1.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/shasta_0.7.0-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/shasta_0.7.0-3.diff.gz is missing [2024-09-27 02:49:40] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/shasta_0.7.0-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/shasta_0.7.0-3.diff.gz is missing [2024-09-27 02:49:40] INFO: Finished at 2024-09-27 02:49:40.968617, took: 0:00:00.507185 Fri Sep 27 02:49:41 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/shasta.html Fri Sep 27 02:49:41 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Sep 27 02:49:41 UTC 2024 I: Submitting 20K b1/shasta_0.12.0-1_amd64.buildinfo.asc https://buildinfo.debian.net/ed19c28e4aac6b13903909ae08b188b4e4180fdc/shasta_0.12.0-1_all Fri Sep 27 02:49:41 UTC 2024 I: Submitting 20K b2/shasta_0.12.0-1_amd64.buildinfo.asc https://buildinfo.debian.net/27e3ed2a8297f1f4e4b2140a5d154508eb47ac2a/shasta_0.12.0-1_all Fri Sep 27 02:49:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Sep 27 02:49:42 UTC 2024 I: Done submitting .buildinfo files. Fri Sep 27 02:49:42 UTC 2024 I: Removing signed shasta_0.12.0-1_amd64.buildinfo.asc files: removed './b1/shasta_0.12.0-1_amd64.buildinfo.asc' removed './b2/shasta_0.12.0-1_amd64.buildinfo.asc' 1727405382 amd64 trixie shasta Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/shasta_0.12.0-1.rbuild.log: 91.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/shasta_0.12.0-1.rbuild.log.gz [2024-09-27 02:49:43] INFO: Starting at 2024-09-27 02:49:43.130628 [2024-09-27 02:49:43] INFO: Generating the pages of 1 package(s) [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/shasta_0.12.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/shasta_0.12.0-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/shasta_0.11.1-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/shasta_0.11.1-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/shasta_0.11.1-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/shasta_0.11.1-1.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/shasta_0.7.0-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/shasta_0.7.0-3.diff.gz is missing [2024-09-27 02:49:43] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/shasta_0.7.0-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/shasta_0.7.0-3.diff.gz is missing [2024-09-27 02:49:43] INFO: Finished at 2024-09-27 02:49:43.542713, took: 0:00:00.412090 All cleanup done. Fri Sep 27 02:49:43 UTC 2024 - total duration: 0h 27m 2s. Fri Sep 27 02:49:43 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2CQKERog, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 27min 6.379s CPU time consumed: 9.020s